They also lost manager Momy Zafran who resigned shortly after the club won promotion, replacing him with Eyal Lahman.

In addition, the club had to play games in Haifa's Kiryat Eliezer Stadium, as their home ground in Sakhnin was deemed unfit for the Premier League.

The team gained a reputation for being a tough, combative outfit, similar in style to the Crazy Gang period at English club Wimbledon.

However, Sakhnin were beaten 7–1 on aggregate, including a 5–1 home defeat in a match played at the Ramat Gan Stadium in Tel Aviv District due to security concerns.

At the annual Land Day ceremony in Sakhnin in the year of 2000, a large crowd of Palestinians were unexplainably tear gassed.

Though events (such as this) coated by such turmoil aggravated those who resided in Sakhnin, their people still attempted to use the soccer stadium as an outlet to ease the relations with those who brought political unrest and corruption.

Despite a large cash injection made by Israeli businessman Arcadi Gaydamak ($400,000) in the hope of promoting peace and harmony among the citizens of Israel,[4] and a return to their rebuilt home stadium (largely financed by the Emir of Qatar, hence the renaming to Doha Stadium), Sakhnin were relegated at the end of 2005–06 season, finishing nine points from safety.

However, with one of the largest budgets in the division (around five and a half million shekels), the club were amongst the favourites to return quickly to the Premier League, and did so by finishing as runners-up to Kiryat Shmona.

Problems due to political unrest in the region caused the club's leadership to ask for the postponement of Intertoto cup matches in the Summer of 2008,[5] Most of the stars of the team were sold, most notably Maor Buzaglo who signed for Maccabi Tel Aviv.

After suffering a 7–0 loss, the greatest defeat in the club's history, the Sakhnin chairman left the administrative division of Ligat Ha'al.

Bnei Sakhnin is also mentioned in the popular Israeli rap song ״רעל עכברים״ (rat poison) by popular Israeli rapper mc fitusi where he says ״הסיכוי שהם ידעו מה בשקיות נמוך כמו בני סכנין בליגת האלופות״ (the chance they’ll realise what’s in the bags is as low as Bnei Sakhnin in the premier league) this reference was met with some backlash and fans noted that it was racist towards Arabs, he later apologised and changed the line.